Tissue culture-based breast cancer biomarker discovery platform

International Journal of Cancer

Volumn 123, Issue 9, 2008, Pages 2007-2012

  Kulasingam, Vathany ^a,b   Diamandis, Eleftherios P ^a,b,c  

^a UNIVERSITY OF TORONTO   (Canada)

^b MOUNT SINAI HOSPITAL   (Canada)

^c UNIVERSITY HEALTH NETWORK   (Canada)

Author keywords

Breast cancer; Cell lines; Mass spectrometry; Secretome; Tumor marker

Indexed keywords

BIOLOGICAL MARKER; TUMOR MARKER;

BODY FLUID; BREAST CANCER; CANCER CELL CULTURE; HUMAN; MASS SPECTROMETRY; NONHUMAN; PATHOPHYSIOLOGY; PLASMA; PRIORITY JOURNAL; PROGNOSIS; PROTEIN SECRETION; PROTEOMICS; REVIEW; SENSITIVITY AND SPECIFICITY; TANDEM MASS SPECTROMETRY; TISSUE CULTURE; TREATMENT RESPONSE; BREAST TUMOR; CULTURE MEDIUM; FEMALE; METHODOLOGY; TUMOR CELL LINE;

BREAST NEOPLASMS; CELL LINE, TUMOR; CULTURE MEDIA; FEMALE; HUMANS; PROTEOMICS; TANDEM MASS SPECTROMETRY; TUMOR MARKERS, BIOLOGICAL;

EID: 51649116693     PISSN: 00207136     EISSN: 10970215     Source Type: Journal    
DOI: 10.1002/ijc.23844     Document Type: Review

References (59)

1. Etzioni R, Urban N, Ramsey S, McIntosh M, Schwartz S, Reid B, Radich J, Anderson G, Hartwell L. The case for early detection. Nat Rev Cancer 2003;3:243-52.
2. Jemal A, Siegel R, Ward E, Hao Y, Xu J, Murray T, Thun MJ. Cancer statistics, 2008. CA Cancer J Clin 2008;58:71-96.
3. Hayes DF, Bast RC, Desch CE, Fritsche H, Jr, Kemeny NE, Jessup JM, Locker GY, McDonald JS, Mennel RG, Norton L, Ravdin P, Taube S, et al. Tumor marker utility grading system: a framework to evaluate clinical utility of tumor markers. J Natl Cancer Inst 1996;88:1456-66.
4. Glish GL, Vachet RW. The basics of mass spectrometry in the twenty-first century. Nat Rev Drug Discov 2003;2:140-50.
5. Steen H, Mann M. The ABC's (and XYZ's) of peptide sequencing. Nat Rev Mol Cell Biol 2004;5:699-711.
6. Marcotte EM. How do shotgun proteomics algorithms identify proteins? Nat Biotechnol 2007;25:755-7.
7. Wright GL, Jr. Two-dimensional acrylamide gel electrophoresis of cancer-patient serum proteins. Ann Clin Lab Sci 1974;4:281-93.
8. Rifai N, Gillette MA, Carr SA. Protein biomarker discovery and validation: the long and uncertain path to clinical utility. Nat Biotechnol 2006;24:971-83.
9. Anderson NL, Anderson NG. The human plasma proteome: history, character, and diagnostic prospects. Mol Cell Proteomics 2002;1:845-67.
10. Bertucci F, Bimbaum D, Goncalves A. Proteomics of breast cancer: principles and potential clinical applications. Mol Cell Proteomics 2006;5:1772-86.
11. Bose R, Molina H, Patterson AS, Bitok JK, Periaswamy B, Bader JS, Pandey A, Cole PA. Phosphoproteomic analysis of Her2/neu signaling and inhibition. Proc Natl Acad Sci USA 2006;103:9773-8.
12. Vargo-Gogola T, Rosen JM. Modelling breast cancer: one size does not fit all. Nat Rev Cancer 2007;7:659-72.
13. Pitteri SJ, Hanash SM. Proteomic approaches for cancer biomarker discovery in plasma. Expert Rev Proteomics 2007;4:589-90.
14. Shao ZM, Nguyen M. Nipple aspiration in diagnosis of breast cancer. Semin Surg Oncol 2001;20:175-80.
15. Wrensch MR, Petrakis NL, Gruenke LD, Ernster VL, Miike R, King EB, Hauck WW. Factors associated with obtaining nipple aspirate fluid: analysis of 1428 women and literature review. Breast Cancer Res Treat 1990;15:39-51.
16. Alexander H, Stegner AL, Wagner-Mann C, Du Bois GC, Alexander S, Sauter ER. Proteomic analysis to identify breast cancer biomarkers in nipple aspirate fluid. Clin Cancer Res 2004;10: 7500-10.
17. Pawlik TM, Hawke DH, Liu Y, Krishnamurthy S, Fritsche H, Hunt KK, Kuerer HM. Proteomic analysis of nipple aspirate fluid from women with early-stage breast cancer using isotope-coded affinity tags and tandem mass spectrometry reveals differential expression of vitamin D binding protein. BMC Cancer 2006;6:68.
18. Varnum SM, Covington CC, Woodbury RL, Petritis K, Kangas LJ, Abdullah MS, Pounds JG, Smith RD, Zangar RC. Proteomic characterization of nipple aspirate fluid: identification of potential biomarkers of breast cancer. Breast Cancer Res Treat 2003;80:87-97.
19. Alldridge L, Metodieva G, Greenwood C, Al Janabi K, Thwaites L, Sauven P, Metodiev M. Proteome profiling of breast tumors by gel electrophoresis and nanoscale electrospray ionization mass spectrometry. J Proteome Res 2008;7:1458-69.
20. Hondermarck H, Tastet C, Yazidi-Belkoura I, Toillon RA, Le Bourhis X. Proteomics of breast cancer: the quest for markers and therapeutic targets. J Proteome Res 2008;7:1403-11.
21. Hondermarck H. Breast cancer: when proteomics challenges biological complexity. Mol Cell Proteomics 2003;2:281-91.
22. Pitteri SJ, Faca VM, Kelly-Spratt KS, Kasarda AE, Wang H, Zhang Q, Newcomb L, Krasnoselsky A, Paczesny S, Choi G, Fitzgibbon M, McIntosh MW, et al. Plasma proteome profiling of a mouse model of breast cancer identifies a set of up-regulated proteins in common with human breast cancer cells. J Proteome Res 2008;7:1481-9.
23. Whiteaker JR, Zhang H, Lei Z, Wang P, Kelly-Spratt KS, Ivey RG, Piening BD, Feng LC, Kasarda E, Gurley KE, Eng JK, Chodosh LA, et al. Integrated pipeline for mass spectrometry-based discovery and confirmation of biomarkers demonstrated in a mouse model of breast cancer. J Proteome Res 2007;6:3962-75.
24. Nandi S, Guzman RC, Yang J. Hormones and mammary carcinogenesis in mice, rats, and humans: a unifying hypothesis. Proc Natl Acad Sci USA 1995;92:3650-7.
25. Chen ST, Pan TL, Juan HF, Chen TY, Lin YS, Huang CM. Breast tumor microenvironment: proteomics highlights the treatments targeting secretome. J Proteome Res 2008;7:1379-87.
26. Hathout Y. Approaches to the study of the cell secretome. Expert Rev Proteomics 2007;4:239-48.
27. Lacroix M, Leclercq G. Relevance of breast cancer cell lines as models for breast tumours: an update. Breast Cancer Res Treat 2004;83:249-89.
28. Martin DB, Gifford DR, Wright ME, Keller A, Yi E, Goodlett DR, Goodlett DR, Aebersold R, Nelson PS. Quantitative proteomic analysis of proteins released by neoplastic prostate epithelium. Cancer Res 2004;64:347-55.
29. Mbeunkui F, Fodstad O, Pannell LK. Secretory protein enrichment and analysis: an optimized approach applied on cancer cell lines using 2D LC-MS/MS. J Proteome Res 2006;5:899-906.
30. Canelle L, Bousquet J, Pionneau C, Hardouin J, Choquet-Kastylevsky G, Joubert-Caron R, Caron M. A proteomic approach to investigate potential biomarkers directed against membrane-associated breast cancer proteins. Electrophoresis 2006;27:1609-16.
31. Xiang R, Shi Y, Dillon DA, Negin B, Horvath C, Wilkins JA. 2D LC/ MS analysis of membrane proteins from breast cancer cell lines MCF7 and BT474. J Proteome Res 2004;3:1278-83.
32. Adam PJ, Boyd R, Tyson KL, Fletcher GC, Stamps A, Hudson L, Poyer HR, Redpath N, Griffiths M, Steers G, Harris AL, Patel S, et al. Comprehensive proteomic analysis of breast cancer cell membranes reveals unique proteins with potential roles in clinical cancer. J Biol Chem 2003;278:6482-9.
33. Patwardhan AJ, Strittmatter EF, Camp DG, Smith RD, Pallavicini MG. Comparison of normal and breast cancer cell lines using proteome, genome, and interactome data. J Proteome Res 2005;4:1952-60.
34. Charafe-Jauffret E, Ginestier C, Monville F, Finetti P, Adelaide J, Cervera N, Fekairi S, Xerri L, Jacquemier J, Birnbaum D, Bertucci F. Gene expression profiling of breast cell lines identifies potential new basal markers. Oncogene 2006;25:2273-84.
35. Sorlie T, Tibshirani R, Parker J, Hastie T, Marron JS, Nobel A, Deng S, Johnsen H, Pesich R, Geisler S, Demeter J, Perou CM, et al. Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc Natl Acad Sci USA 2003;100:8418-23.
36. Sorlie T, Perou CM, Tibshirani R, Aas T, Geisler S, Johnsen H, Hastie T, Eisen MB, van de Rijn M, Jeffrey SS, Thornsen T, Quist H, et al. Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci USA 2001;98:10869-74.
37. Abd El-Rehim DM, Ball G, Pinder SE, Rakha E, Paish C, Robertson JF, Macmillan D, Blamey RW, Ellis IO. High-throughput protein expression analysis using tissue microarray technology of a large well-characterised series identifies biologically distinct classes of breast cancer confirming recent cDNA expression analyses. Int J Cancer 2005;116:340-50.
38. Jacquemier J, Ginestier C, Rougemont J, Bardou VJ, Charafe-Jauffret E, Geneix J, Adélaide J, Koki A, Houvenaeghel G, Hassoun J, Maraninchi D, Viens P, et al. Protein expression profiling identifies subclasses of breast cancer and predicts prognosis. Cancer Res 2005;65:767-79.
39. Neve RM, Chin K, Fridlyand J, Yeh J, Baehner FL, Fevr T, Clark L, Bayani N, Coppe JP, Tong F, Speed T, Spellman PT, et al. A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes. Cancer Cell 2006;10:515-27.
40. Kulasingam V, Diamandis EP. Proteomics analysis of conditioned media from three breast cancer cell lines: a mine for biomarkers and therapeutic targets. Mol Cell Proteomics 2007;6:1997-2011.
41. Soule HD, Maloney TM, Wolman SR, Peterson WD, Jr, Brenz R, McGrath CM, Russo J, Pauley RJ, Jones RF, Brooks SC. Isolation and characterization of a spontaneously immortalized human breast epithelial cell line. MCF-10. Cancer Res 1990;50:6075-86.
42. Lasfargues EY, Coutinho WG, Redfield ES. Isolation of two human tumor epithelial cell lines from solid breast carcinomas. J Natl Cancer Inst 1978;61:967-78.
43. Slamon DJ, Clark GM, Wong SG, Levin WJ, Ullrich A, McGuire WL. Human breast cancer: correlation of relapse and survival with amplification of the HER-2/neu oncogene. Science 1987;235:177-82.
44. Cailleau R, Olive M, Cruciger QV. Long-term human breast carcinoma cell lines of metastatic origin: preliminary characterization. In Vitro 1978;14:911-5.
45. She QB, Solit D, Basso A, Moasser MM. Resistance to gefitinib in PTEN-null HER-overexpressing tumor cells can be overcome through restoration of PTEN function or pharmacologic modulation of constitutive phosphatidylinositol 3′-kinase/Akt pathway signaling. Clin Cancer Res 2003;9:4340-6.
46. Panigrahi AR, Pinder SE, Chan SY, Paish EC, Robertson JF, Ellis IO. The role of PTEN and its signalling pathways, including AKT, in breast cancer; an assessment of relationships with other prognostic factors and with outcome. J Pathol 2004;204:93-100.
47. Mbeunkui F, Metge BJ, Shevde LA, Pannell LK. Identification of differentially secreted biomarkers using LC-MS/MS in isogenic cell lines representing a progression of breast cancer. J Proteome Res 2007;6:2993-3002.
48. Jacobs JM, Waters KM, Kathmann LE, Camp Ii DG, Wiley HS, Smith RD, Thrall BD. The mammary epithelial cell secretome and its regulation by signal transduction pathways. J Proteome Res 2008;7:558-69.
49. Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, Mann M. Stable isotope labeling by amino acids in cell culture. SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 2002;1:376-86.
50. Liang X, Zhao J, Hajivandi M, Wu R, Tao J, Amshey JW, Pope RM. Quantification of membrane and membrane-bound proteins in normal and malignant breast cancer cells isolated from the same patient with primary breast carcinoma. J Proteome Res 2006;5:2632-41.
51. Chen Y, Choong LY, Lin Q, Philp R, Wong CH, Ang BK, Tan YL, Loh MC, Hew CL, Shah N, Drujer BJ, Chong PK, et al. Differential expression of novel tyrosine kinase substrates during breast cancer development. Mol Cell Proteomics 2007;6:2072-87.
52. Porter DA, Krop IE, Nasser S, Sgroi D, Kaelin CM, Marks JR, Riggins G, Polyak K. A SAGE (serial analysis of gene expression) view of breast tumor progression. Cancer Res 2001;61:5697-5702.
53. Dombkowski AA, Cukovic D, Novak RF. Secretome analysis of microarray data reveals extracellular events associated with proliferative potential in a cell line model of breast disease. Cancer Lett 2006;24149-58.
54. Celis JE, Gromov P, Cabezon T, Moreira JM, Ambartsumian N, Sandelin K, Rank F, Gromova I. Proteomic characterization of the interstitial fluid perfusing the breast tumor microenvironment: a novel resource for biomarker and therapeutic target discovery. Mol Cell Proteomics 2004;3:327-44.
55. Bast RC, Jr, Klug TL, St John E, Jenison E, Niloff JM, Lazarus H, Berkowitz RS, Leavitt T, Griffiths CT, Parker L, Zurawski VR, Jr, Knapp RC. A radioimmunoassay using a monoclonal antibody to monitor the course of epithelial ovarian cancer. N Engl J Med 1983;309:883-7.
56. Petricoin EF, Liotta LA. Clinical applications of proteomics. J Nutr 2003;133:2476S-84S.
57. Shaw KR, Wrobel CN, Brugge JS. Use of three-dimensional basement membrane cultures to model oncogene-induced changes in mammary epithelial morphogenesis. J Mammary Gland Biol Neoplasia 2004;9:297-310.
58. Lee GY, Kenny PA, Lee EH, Bissell MJ. Three-dimensional culture models of normal and malignant breast epithelial cells. Nat Methods 2007;4:359-65.
59. Hagemann T, Robinson SC, Schulz M, Trumper L, Balkwill FR, Binder C. Enhanced invasiveness of breast cancer cell lines upon cocultivation with macrophages is due to TNF-alpha dependent up-regulation of matrix metalloproteases. Carcinogenesis 2004;25:1543-9.